PyPy 2.0 has numpy.dot now, but not numpy.linalg
Add comment to tutorial doctest regarding PyPy

No need for TravisCI [ci skip]
One central import for this test
Test Bio.Motif & Bio.motifs PSSM with alternative alphabet.

Addresses this issue: http://www.biostars.org/p/73500/
http://lists.open-bio.org/pipermail/biopython-dev/2013-June/010639.html
Fix motif alphabet instance bug

Previous commit was a test for this bug, addresses
http://www.biostars.org/p/73500/
http://lists.open-bio.org/pipermail/biopython-dev/2013-June/010639.html
Remove now redundant imports